Merge pull request #574 from hubmapconsortium/expose_creation_action_…

…from_activity

Add Dataset Activity.creation_action to ENTITY.Dataset as creation_action_activity

entity-api-spec.yaml

@@ -754,6 +754,9 @@ components:
         dbgap_study_url:
           type: string
           description: 'A URL linking the dataset to the particular study on dbGap it belongs to'
+        creation_action:
+          type: string
+          description: 'The associated action that represents the creation of that dataset'
     Upload:
       type: object
       properties:

src/schema/provenance_schema.yaml

@@ -281,6 +281,7 @@ ENTITIES:
         type: string
         transient: true
         immutable: true
+        on_read_trigger: get_creation_action_activity
         description: "The activity that was performed."
         before_property_create_validators:
           - validate_creation_action

src/schema/schema_manager.py

@@ -115,7 +115,7 @@ def load_provenance_schema(valid_yaml_file):
     with open(valid_yaml_file) as file:
         schema_dict = yaml.safe_load(file)
 
-        logger.info("Schema yaml file loaded successfully")
+        logger.info(f"Provenance Schema yaml file loaded successfully from {valid_yaml_file} :)")
 
         return schema_dict
 

src/schema/schema_neo4j_queries.py

@@ -485,6 +485,20 @@ def get_entity_type(neo4j_driver, entity_uuid: str) -> str:
     return None
 
 
+def get_entity_creation_action_activity(neo4j_driver, entity_uuid: str) -> str:
+    query: str = f"MATCH (ds {{uuid:'{entity_uuid}'}})<-[:ACTIVITY_OUTPUT]-(a:Activity) RETURN a.creation_action"
+
+    logger.info("======get_entity_creation_action() query======")
+    logger.info(query)
+
+    with neo4j_driver.session() as session:
+        record = session.read_transaction(execute_readonly_tx, query)
+        if record and len(record) == 1:
+            return record[0]
+
+    return None
+
+
 """
 Create or recreate one or more linkages (via Activity nodes) 
 between the target entity node and the direct ancestor nodes in neo4j

src/schema/schema_triggers.py

@@ -1151,6 +1151,20 @@ def get_next_revision_uuid(property_key, normalized_type, user_token, existing_d
     return property_key, next_revision_uuid
 
 
+def get_creation_action_activity(property_key, normalized_type, user_token, existing_data_dict, new_data_dict):
+    if 'uuid' not in existing_data_dict:
+        raise KeyError("Missing 'uuid' key in 'existing_data_dict' during calling 'get_creation_action_activity()' trigger method.")
+
+    uuid: str = existing_data_dict['uuid']
+    logger.info(f"Executing 'get_creation_action_activity()' trigger method on uuid: {uuid}")
+
+    neo4j_driver_instance = schema_manager.get_neo4j_driver_instance()
+    creation_action_activity =\
+        schema_neo4j_queries.get_entity_creation_action_activity(neo4j_driver_instance, uuid)
+
+    return property_key, creation_action_activity
+
+
 """
 Trigger event method to commit thumbnail file saved that were previously uploaded via ingest-api